Ultimate Phaser Tool (Borland Genetics)
The Ultimate Phaser tool provides Borland Genetics users direct access to the software's phasing engine. The Ultimate Phaser provides three types of phased mono output, i.e. a DNA kit consisting of the in-phase alleles across the genome, and the two out-of-phase alleles (often referred to as out-of-phase and evil twin). Output is produced without regard for whether the input DNA kits meet matching criteria, and inconsistent calls result in no-calls in the output. Therefore, for cases other than the parent-child scenario, the output kits must be manually "bound" to the HIR matching regions. This is typically accomplished via the Matching Segments tool. Output from the Ultimate Phaser tool is assigned a female gender by default. When the tool is used to compare parents to children, while binding is not necessary, it is recommended that gender be assigned in the Resource Manager so that when the synthetic output resources are used as input for other tools, the X-chromosome is handled properly. Application to Typical Workflows The most common (and most simple) application of the Ultimate Phaser tool is to create Mono kits for use in visual phasing projects. These visual phasing data kits should always be marked as research kits when uploaded to GEDmatch, as they do not typically represent the reconstruction of a single real person. Visual phasing data kits are typically full Mono kits that include data from one of the following three categories of phased data: * Parent ∩ Child (all DNA shared between a parent and child, which will alternate between grandparent streams at recombination points determined via visual phasing) * Parent x Child (sometimes referred to as the evil twin, all DNA not passed from a parent to a child, which will also alternate between grandparent streams at recombination points, but with opposite phase as the previous category) * Child x Parent (representing the DNA inherited from the opposite parent, not generally used in visual phasing, but that can be mapped using DNAPainter and the GedMatch matching segments tool, and an excellent choice for use with the Borland Genetics Extract Segments tool) Visual phasing is an important technique at the heart of any multi-generation reconstruction project. Unbound Nature of Ultimate Phaser Output The Ultimate Phaser tool allows the user access to unbound phased data directly from the Borland Genetics Phasing engine. Output from the Ultimate Phaser tool, being unbound, may not accurately reflect the DNA of any real person, and is thus assigned a default gender of female to allow the most liberal X chromosome inclusion rules when used with other tools. (Of course, gender can be edited in the Resource Manager if desired). When the Ultimate Phaser is used to phase parents and children, the unbound data is ordinary since the child and parent should match across the entire genome. However, the unbound nature of the phased output becomes apparent when the tool is used to phase relatives of other degrees of relatedness. This is because the kits will be phased against each-other over the entire genome, whether segments match with one another or not (with conflicts replaced with no-calls). Note: where full siblings match FIR, the output data will be meaningless and must be filtered. A Reconstructed Segments data file is NOT created along with the phased output data. To reconstruct a subset of segments where relatives match eachother (HIR), one must create one's own filter by choosing coordinates to define a filter in GedMatch using a 1:1 compare between the relatives with whatever thresholds deemed appropriate for the situation. One can then copy the 1:1 data in to DNAPainter and apply the filter via the “Extract Segments” tool. One can even experiment with different thresholds (say 5 cM vs. 7 cM vs. 10 cM) and copy the boundaries as separate filters within the DNAPainter profile and compare the resulting segments. The GedMatch matching segment tool can be used to assist in determining the validity of smaller segments and selective remove them from the DNAPainter profile as appropriate before binding (Binding=applying the filter and replacing unfiltered regions with white noise using the “Extract Segments” tool). Category:Autosomal DNA Category:Borland Genetics